› 4rz8

X-ray diffraction
1.9Å resolution

Crystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist

Released:
DOI: 10.2210/pdb4rz8/pdb
PDB entry 4rz8 coloured by chain, front view.
PDB entry 4rz8 coloured by chain, side view.
PDB entry 4rz8 coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Structure-Based Design of a Small Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity.
Curreli F, Kwon YD, Zhang H, Scacalossi D, Belov DS, Tikhonov AA, Andreev IA, Altieri A, Kurkin AV, Kwong PD, Debnath AK
J Med Chem 58 6909-6927 (2015)
PMID: 26301736

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102400 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Human immunodeficiency virus 1 envelope glycoprotein Gp120 domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 353 amino acids
Theoretical weight: 39.16 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0M3KKW9 (Residues: 1-80, 83-185, 192-353; Coverage: 98%)
Gene name: HIV-1 Env
Sequence domains: Envelope glycoprotein GP120
Structure domains: Human immunodeficiency virus 1, Gp160, envelope glycoprotein

Ligands and Environments

3 bound ligands:
Ligand NAG 40 x NAG
Ligand 3ZM 4 x 3ZM
Ligand EPE 4 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 113.621Å b: 68.842Å c: 116.192Å
α: 90° β: 110.59° γ: 90°
R-values:
R R work R free
0.227 0.227 0.244
Expression system: Homo sapiens

Quick links

Citations

7 review citations

HIV-1 Entry and Membrane Fusion Inhibitors.
Xiao et al. (2021)
6 more

2 mentions without citation

Structure-Based Design of a Small Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity.
Curreli et al. (2015)
1 more